Download the ispconfig 3 tar.gz and run the update.php script. Choose to reconfigure services during update.

Such problems are commoin when you update Centos as YUM destroys the existing configuration during update. For that reason you should consider to use Debian in case that you install a new server in future as the Debian.

Update: This is because I changed my mysql root password. There were two options to solve it:
1) Either I make changes in /usr/local/ispconfig/server/mysqlclient_db.conf and append the new password; But still configs the /usr/local/ispconfig/interface/ folder needed to be changed either.

2) Therefore, I took an easy way: I changed the mysql root password to the old one.